I would recommend "ASP dot NET Storefront". It's not open source, but you can purchase the source if you like. This is what I use to run my eCom site. Also has excellent SEO support and good integration with payment gateways, shipping carriers and more.

I haven't seen v5 of Miva Merchant, but v4 would let you create multiple storefronts with separate payment, shipping, tax, customer records, and order fulfillment. I would think all that is still available in v5.